“That was actually pretty refreshing.” At least that’s what graduate student Joe Russell claimed as he dried off after his brief dip in Pavilion Lake. He wasn’t shivering, and his lips weren’t blue, but the look on his face when he first jumped in had definitely been one of shock.

Russell studies marine biosciences at the University of Delaware (UD). His advisor, Jennifer Biddle, is a UD associate professor of marine biosciences. They had devised an experiment, part of Russell’s masters thesis, to see how microorganisms that live on Pavilion Lake microbialites would respond to being moved from their native habitat in the depths of the lake to a shallower location.

Earlier in the week, scuba divers had collected microbialites from three different depths in Pavilion Lake: 35, 65 and 85 feet. Russell had placed these samples in rectangular plastic bins and stashed them a short ways offshore, near the boat dock of a local resident, at a depth of 4.5 feet. This was his and Biddle’s first trip back to retrieve some of the samples for analysis. Feeling nostalgic for Pavilion Lake, I tagged along.

Why he hadn’t just tied a rope to the bins so he could haul them up onto the boat dock without having to take the plunge, I have no idea. So Russell dove into the water, and then half-swam, half-carried the bins, one at a time, to the dock, where Biddle, sensibly warm and dry, was waiting to grab small chunks of microbialite from the bins and seal them into sterile plastic bags.

Russell wants to see whether, within the space of a week, he can detect changes in the microbial populations that live on the microbialites caused by changes in the microbes’ place of residence. He’ll take samples from his experiment two more times, each time freezing the samples to preserve their present state until he can get them back to the lab, grind them up and analyze them, comparing them to each other and to previously collected samples from Pavilion Lake and samples collected this year from Kelly Lake.

He plans to follow three lines of investigation: DNA, RNA and biological pigments.

DNA? Changes in DNA in a week? “Microbial communities,” Biddle said, “can double every 20 minutes.… We could possibly see a change in the DNA if, let’s say, there’s a bloom, if one of the species loves the light we’ve given them,” – more light is available in the shallows than deeper down in the lake – “and grows up and takes over, at the end of a week, you could have a complete changeover in the microbial community.”

But that’s not likely, Biddle conceded, “because these microbialites are so old. They grow slowly. I don’t think we’ll have a complete change, but we might see a significant shift in patterns.”

Besides, said Russell, looking at the DNA “just tells us if the genes are there or not. But to understand whether they’re actively expressed and the levels of expression,” that requires looking at RNA. RNA can tell you what the organisms are doing.

Some of the dozens of microbialites retrieved by scuba divers from Kelly Lake. Credit: Henry Bortman

We moved on to RNA. Whereas looking at the DNA in a sample tells you which organisms are there, and what they’re capable of, looking at RNA tells you what they’re actually doing, which of their genes are being expressed. So even if the demographics of the microbial population don’t shift noticeably, some organisms might start behaving differently.

Every microbe has a large storehouse of genes, but only a fraction of them are active at any given time. When environmental conditions change – when a microbe is suddenly taken from the dingy depths of a lake and flooded with sunlight, for example – it can shift gears, turning off one set of genes and turning on another.

But studying RNA is a tricky proposition. For one thing, Russell says, it’s “inherently more unstable” than DNA; it breaks down easily. And even when the RNA remains stable enough to detect, all the RNA in a sample gets mixed together. You can’t necessarily tell which organism it comes from. “Trying to pick out a specific signal in the RNA pool might not be that easy,” Biddle said. “So that’ll be sort of the icing on the cake if it does happen.”

Which is why Russell and Biddle are also interested in looking at pigments. One of the principal organisms suspected of playing a role in the formation of Pavilion and Kelly Lake microbialites are photosynthetic cyanobacteria. “Cyanobacteria harvest light using pigments. And even within one species,” Biddle said, they can have as many as “three or four different sort of life styles in terms of how they’re harvesting light,” using different pigments to harvest light at different wavelengths, depending on what’s available.

“No-one’s really ever looked at the pigments in Pavilion,” Biddle said. But it’s just possible they could hold a key to understanding why microbialites in different locations – and now in different lakes – look so different from each other.

Perhaps the same microbes, with the same genetic potential, are ubiquitous, but are behaving differently under different conditions. In “If we see these significant shifts in pigment, in life strategy, within a week, that could explain a number of things,” Russell said.

Of course, they may not see anything in a week. Which may mean that pigments are not the key to the puzzle. Or it could simply mean that a week isn’t long enough for them to show their stuff.

The microbialites in Pavilion and Kelly Lakes grow very slowly. They’ve been around for thousands of years. Scientists have been studying them for less than a decade. While the scientists may be anxious to unlock the microbes’ secrets, the microbes themselves have no particular reason to rush.

PLRP field operations will continue through the rest of the week. If you have a question for someone on the PLRP team, click the red Ask a Question button and send it in. We’ll get you an answer as quickly as we can.